Using metabarcoding to compare the suitability of two blood‐feeding leech species for sampling mammalian diversity in North Borneo

The application of high‐throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood‐feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. To address these questions, we collected spatially matched samples of two congeneric leech species Haemadipsa picta and Haemadipsa sumatrana from lowland rainforest in Borneo. For each species, we pooled ~500 leeches into batches of 10 individuals, performed PCR to target a section of the mammalian 16S rRNA locus and undertook sequencing of amplicon libraries using an Illumina MiSeq. In total, we identified sequences from 14 mammalian genera, spanning nine families and five orders. We found greater numbers of detections, and higher diversity of OTUs, in H. picta compared with H. sumatrana, with rodents only present in the former leech species. However, comparison of samples from across the landscape revealed no significant difference in mammal community composition between the leech species. We therefore suggest that H. picta is the more suitable iDNA sampler in this degraded Bornean forest. We conclude that the choice of invertebrate sampler can influence the detectability of different mammal groups and that this should be accounted for when designing iDNA studies.     

Habitat preferences of small mammals in tropical open-forest of the Northern Territory

Pattern analysis was used to investigate the habitat preferences of five small mammal species in tropical open-forest of the Northern Territory. Fifty-one sites were classified by faunal abundance and the groups examined for significant differences in vegetation structural attributes and plant species in both dry and wet seasons. The omnivore Isoodon macrourus showed strong association with floristic and vegetation structural attributes only in the dry season, when areas with a dense understorey of small trees and shrubs and a high percentage of leaf litter cover were favoured. Of the two primarily carnivorous species, Antechinus bellus was related strongly with floristic and structural attributes in both seasons and showed a consistent preference for areas with relatively dense low-level foliage (< 2m). By contrast, Dasyurus hallucatus was associated more with the structurally simple open-forest types. Of the two mainly herbivorous species Mesembdomys gouldii showed associations only withfioristics in both seasons, while the habitat relationships of Trichosurus arnhemensis were very weak due to its low abundance in the study area. The number and strength of animal/habitat relationships were greatest in the dry season. Forest types with dense mid-level foliage and abundant hollow logs and leaf litter had the greatest mammal richness and abundance; these areas may be critical to the survival of local mammal populations. A comparison of site-groups, defined independently on the basis of fauna, floristics or structure, showed that animal groups overlapped one to six of the habitat groups. The animal's perception of s‘habitat’ may thus differ from that of humans, or that defined by measurement of habitat attributes.     

Can Saturniidae moths be bioindicators? Spatial and temporal distribution in the Brazilian savannah

Some moths species are considered good indicators of habitat quality because they are very responsive to human disturbance, vegetation type, and successional processes. However, Saturniidae moths have not yet been considered as indicators of environmental quality. Little is known on the distribution of moth species in different vegetation types and the moths’ seasonal variations in the Brazilian savannah. Therefore, this study aims to describe the spatial distribution and temporal patterns of moths belonging to the Saturniidae family in two vegetation types—Cerrado sensu stricto on rocky outcrops and semi-deciduous forest—in both the rainy and dry seasons. It addresses the influence of the climatic seasons and vegetation types on abundance, richness, and species composition to describe the temporal and spatial distribution patterns and the relationship between the ecological aspects and the life history of these moths. This study was conducted in the Cerrado phytogeographical domain, in Pireneus State Park, Goiás, Brazil. The results revealed that most Saturniidae species sampled are present during the rainy season and typically found in forest habitats. Furthermore, a clear positive connection was found between the abundance pattern and rainfall seasonality and humid habitats; this is apparently related to the physiological tolerance of these moths, due to rudimentary mouthparts during their adulthood. Thus, rainfall and a forest habitat are important to and fundamental requirements for the persistence of the Saturniidae species in the Cerrado domain. Based on the results of this study, we suggest the use of saturniid species as indicators of changes in vegetation and climatic conditions.     

Bloodlines: mammals,leeches, and conservation in southern Asia

Southern Asia is a biodiversity hotspot both for terrestrial mammals and for leeches. Many small-mammal groups are under-studied in this region, while other mammals are of known conservation concern. In addition to standard methods for surveying mammals, it has recently been demonstrated that residual bloodmeals within leeches can be sequenced to find mammals in a given area. While these invertebrate-parasite-derived DNA (iDNA) methods are promising, most of the leech species utilized for this type of survey remain unevaluated, notwithstanding that their diversity varies substantially. Here we examine approximately 750 individual leech specimens in the genus Haemadipsa across a large range in southern Asia (Bangladesh, Cambodia, and China), specifically reviewing the diversity of mammals they feed on and their own genetic structuring. Leeches were found to feed on a considerable variety of mammals, corroborating prior studies. Additionally, leeches were found to have fed both on bats and on birds, neither of which has previously been recorded with this method. The genetic structuring of the leeches themselves revealed 15 distinct clades of which only two precisely corresponded to previously characterized species, indicating that much work is needed to finalize classifications in this genus. Most importantly, with regards to mammal conservation, leeches in these clades appear to feed on a broad range of mammals.     

Molecular Identification of Haemadipsa rjukjuana (Hirudiniformes: Haemadipsidae) in Gageo Island,Korea

There are 60 species of blood-feeding land leeches, 50 species belonging to the family Haemadipsidae and 10 species belonging to the family Xerobdellidae. Despite recent papers on the land leeches, their taxonomic identification is not fully understood, especially at a species level. In Korea, there have been no historical records of the terrestrial leeches, but recently an unrecorded blood-feeding land leech was discovered at Gageo-do (Island), Korea. Molecular analysis was used to identify the species of 29 leeches collected from Mt. Dock-Sil in Gageo-do. Conventional PCR was conducted using nuclear 18S rRNA and mitochondrial cytochrome c oxidase subunit 1 (CO1) genetic marker. The 18S rRNA sequences revealed that the leeches share 99.9% identity with Haemadipsa rjukjuana (inhabiting Taiwan), and the CO1 sequences revealed that the leeches are very close to H. rjukjuana (inhabiting Taiwan). The CO1 sequences were separated into 2 categories, 1 with 94.6% and the other with 94.3% similarity to the H. rjukjuana L00115A (inhabiting Taiwan). This new finding of the land leech is the first record in Korea. In addition, the north range of the distribution of the blood-feeding leech (Hirudiniformes: Haemadipisidae) should be reconsidered including Korea.     

Influence of Fire Mosaics,Habitat Characteristics and Cattle Disturbance on Mammals in Fire-Prone Savanna Landscapes of the Northern Kimberley

Patch mosaic burning, in which fire is used to produce a mosaic of habitat patches representative of a range of fire histories (‘pyrodiversity’), has been widely advocated to promote greater biodiversity. However, the details of desired fire mosaics for prescribed burning programs are often unspecified. Threatened small to medium-sized mammals (35 g to 5.5 kg) in the fire-prone tropical savannas of Australia appear to be particularly fire-sensitive. Consequently, a clear understanding of which properties of fire mosaics are most instrumental in influencing savanna mammal populations is critical. Here we use mammal capture data, remotely sensed fire information (i.e. time since last fire, fire frequency, frequency of late dry season fires, diversity of post-fire ages in 3 km radius, and spatial extent of recently burnt, intermediate and long unburnt habitat) and structural habitat attributes (including an index of cattle disturbance) to examine which characteristics of fire mosaics most influence mammals in the north-west Kimberley. We used general linear models to examine the relationship between fire mosaic and habitat attributes on total mammal abundance and richness, and the abundance of the most commonly detected species. Strong negative associations of mammal abundance and richness with frequency of late dry season fires, the spatial extent of recently burnt habitat (post-fire age <1 year within 3 km radius) and level of cattle disturbance were observed. Shrub cover was positively related to both mammal abundance and richness, and availability of rock crevices, ground vegetation cover and spatial extent of ≥4 years unburnt habitat were all positively associated with at least some of the mammal species modelled. We found little support for diversity of post-fire age classes in the models. Our results indicate that both a high frequency of intense late dry season fires and extensive, recently burnt vegetation are likely to be detrimental to mammals in the north Kimberley. A managed fire mosaic that reduces large scale and intense fires, including the retention of ≥4 years unburnt patches, will clearly benefit savanna mammals. We also highlighted the importance of fire mosaics that retain sufficient shelter for mammals. Along with fire, it is clear that grazing by introduced herbivores also needs to be reduced so that habitat quality is maintained.     

Responses of two species of heathland rodents to habitat manipulation: Vegetation density thresholds and the habitat accommodation model

The abundance of two native rodent species, Rattus lutreolus and Pseudomys gracilicaudatus, has been shown to correlate with vegetation density in coastal wet heath. Fox's habitat accommodation model relates relative abundances of such small mammal species to heathland vegetation regeneration following disturbance. Implicit in the model is recognition that it is successional changes in vegetation, not time per se, that drives the responses of small mammal species along a regeneration axis. Using a brush‐cutter we deliberately removed approximately 85% of vegetation around trapping stations and recorded significant reductions in the abundance of both P. gracilicaudatus (an earlier‐stage colonizing species) and R. lutreolus (a late seral‐stage species). A significant decrease in the abundance of only the latter had been demonstrated previously when 60–70% of the vegetation had been removed. Following the brush‐cutting both species re‐entered the mammalian secondary succession at different times, first P. gracilicaudatus followed by R. lutreolus after the vegetation cover thresholds of each species had been reached. The impact of this habitat manipulation experiment was to produce a retrogression of the small mammal succession, experimentally demonstrating causality between changes in vegetation density and subsequent small mammal habitat use.     

Seasonal abundance and habitat use of bird species in and around Wondo Genet Forest,south‐central Ethiopia

The habitat use and seasonal migratory pattern of birds in Ethiopia is less explored as compared to diversity studies. To this end, this study aimed at investigating the patterns of distribution related to seasonality and the effect of habitat characteristics (elevation, slope, and average vegetation height) on habitat use of birds of Wondo Genet Forest Patch. A stratified random sampling design was used to assess the avian fauna across the four dominant habitat types found in the study area: natural forest, wooded grassland, grassland, and agroforestry land. A point transect count was employed to investigate avian species richness and abundance per habitat type per season. Ancillary data, such as elevation above sea level, latitude and longitude, average vegetation height, and percent slope inclination, were recorded with a GPS and clinometers per plot. A total of 33 migratory bird species were recorded from the area, of which 20 species were northern (Palearctic) migrants while 13 were inter‐African migrants. There was a significant difference in the mean abundance of migratory bird species between dry and wet seasons (t = 2.13, p = .038, df = 44). The variation in mean abundance per plot between the dry and wet seasons in the grassland habitat was significant (t = 2.35, p = .051, df = 7). In most habitat types during both dry and wet seasons, omnivore birds were the most abundant. While slope was a good predictor for bird species abundance in the dry season, altitude and average vegetation height accounted more in the wet season. The patch of forest and its surrounding is an important bird area for migratory, endemic, and global threatened species. Hence, it is conservation priority area, and the study suggests that conservation coupled with ecotourism development is needed for its sustainability.     

Fire-created habitats support large mammal community in a Mediterranean landscape

Large mammals play significant roles in shaping the trophic structure of terrestrial ecosystems and affect the form of vegetation growth in many habitats. We studied large mammal community in a Mediterranean habitat mosaic generated by fires originally dominated by pine forests. We conducted camera-trapping surveys in three study sites with different fire histories, and we recorded eight large mammal species including brown bear (Ursus arctos), caracal (Caracal caracal), and wild goat (Capra aegagrus), which are of conservation importance. The mammal community found in the study sites was functionally diverse, including herbivores, omnivores, carnivores, seed dispersers, soil diggers, main preys, and top predators. The site burned 13 years ago had higher species richness than can be expected from a random pattern, but this was not the case in 30- and >40-year-old sites, showing the importance of relatively younger sites for large mammals. Eurasian badger had more probability to have more abundance in places with more open vegetation while wild goat had higher abundance in more dense vegetation. Young individuals of wild goat, brown bear, and wild boar were also detected in the study sites. The results indicate that burned habitats harbor a phylogenetically and functionally diverse large mammal community in landscapes originally dominated by Mediterranean pine forests. Therefore, these forests continue to retain importance for the large mammals after the fire, and burned habitats should be taken into consideration for the conservation and management plans together with mature forests in Mediterranean ecosystems.     

Species assemblages of cyclopoid Copepoda from Mantecal,Venezuela

A 14 year monitoring of species composition and abundance of cyclopoid copepods throughout the rainy and dry seasons in a flooded savanna at Mantecal, Apure State, Venezuela, is presented. Two characteristic habitats within these water bodies were selected: the open center of small ponds free of emergent vegetation and the surrounding flooded grassland. In total, 13 species were registered, all of which appeared in the flooded grassland and 11 of which occurred in the open water. Ten species were common for the two habitats during the dry season. The highest abundance was found in flooded grassland during the dry season. Eight species showed abundances greater than 1.0 individual per liter in flooded grassland during both seasons; 3 and 7 species were this abundant in the open water during rainy and dry seasons, respectively. Mesocyclops meridianus and Microcyclops varicans were the most abundant species in both habitats and seasons, while Thermocyclops decipiens was the dominant species during rainy season in open water. Principal component analysis indicates that the important species were positively correlated between them (sharing habitat and season).     

Density and behaviour of Whinchats Saxicola rubetra on African farmland suggest that winter habitat conditions do not limit European breeding populations

The Whinchat Saxicola rubetra is an Afro‐Palaearctic migrant undergoing widespread population decline. Whinchats winter in West Africa but there are almost no data on their habitat use and behaviour there that may help to explain the cause of this decline. We measured the density of Whinchats, the habitat characteristics associated with their occurrence on farmland, and the relationships between behavioural and habitat variation on farmland around Jos, central Nigeria, over three winters. Whinchats occurred in many fields harvested in the dry season, the density at three sites varying from 0.03 to 0.43 birds/ha, but they were absent at a fourth site. Whinchats were less likely to be found in farmland without particular crops (e.g. structural stem crops such as maize and millet), with more trees, lower amounts of short vegetation (grass, weeds, crops and crop stubble less than 10 cm in height), and higher amounts of medium vegetation (coverage of vegetation 10–100 cm in height) and litter (dead, unburned, vegetation on the ground). Whinchat abundance in areas of farmland where they were present was independent of most variables considered, but density was higher where there was more short vegetation cover. Foraging behaviour did not vary significantly between farmland habitats. All predictors were consistent between season, years and across sites. The presence/absence model was very poor at predicting presence and there were no strong predictors of abundance or foraging variation. This is consistent with a species well below carrying capacity within its environment so that many suitable areas do not have birds present and there is little aggregation at better sites. Overall, Whinchats were abundant and appeared to have plentiful habitat; densities have probably increased alongside the intensification of agriculture (presence of fallow farmland, short vegetation and structural crops). The results suggest that West African farmland in the dry season can support large numbers of Whinchats and that recent population declines in Europe are unlikely to be caused primarily by lack of suitable wintering habitat.     

Fire‐mediated niche‐separation between two sympatric small mammal species

Fire is a key ecological process influencing the population dynamics of small mammals. Whilst shifting competitive advantage amongst small mammal species following a single fire event is well‐documented, there has been little investigation of the potential influence of fire frequency on small mammal interspecific interactions. In this study, we investigated the effect of fire frequency on the abundance of two small dasyurid mammals, Antechinus stuartii and A. flavipes, which occur sympatrically in some parts of their range. The two antechinus species are known to have different habitat preferences, so it is possible that fire regimes may promote their coexistence in areas of sympatry by altering vegetation structure. To investigate this possibility, we estimated the abundance of both species using replicate sites which differed in the number of times burnt (1–4) during the last four decades, but with identical time‐since‐fire. Proportionally, we captured greater numbers of A. stuartii in less frequently burnt sites and greater numbers of A. flavipes in more‐frequently burnt sites. Hence, fire may mediate niche‐separation between these two species. To clarify further this pattern of response to fire frequency, we investigated which structural habitat variables differed between fire frequencies, and compared antechinus abundances with structural vegetation characteristics. We found a trend for lower ground cover density under higher fire frequencies. This offers one potential explanation of the patterns of abundance that we observed. Our study provided insights into the complexities of small mammal responses to fire, and strongly suggests that fire could mediate competitive interactions between species.     

Patterns of bird abundance and habitat use in rice fields of the Kanto Plain, central Japan

Rice fields, the most widespread cropland in Japan, provide important habitat for birds, but few studies have examined bird communities that are influenced by agriculture in rice fields. I studied the seasonal pattern of bird abundance and their habitat preferences in terms of agricultural habitats in the rice fields of the central Kanto Plain, central Japan. In total, 19 waterbird species and 31 landbird species were recorded over the study year. Waterbird occurrence was largely restricted to the cultivation season (i.e. the flooded season, May–August), with maximum abundance in August. Rice fields dried up during winter and supported few waterbirds except for irregular occurrences of little egrets (Egretta garzetta) and common snipes (Gallinago gallinago), which selectively used ditches with shallow water. Landbird abundance increased after the start of cultivation (May) to August, but more birds were attracted to the rice fields in midwinter (around January). For both waterbirds and landbirds, most species preferred levees and fallow grass fields, but avoided fields with rice vegetation. Unplowed fields after harvest were preferred by several species including skylarks (Alauda arvensis), while plowed fields were less attractive to most species. These results suggest the need for advanced agricultural practices to include improvement in habitat quality for birds.     

Does sex matter? Gender‐specific responses to forest fragmentation in Neotropical bats

Understanding the consequences of habitat modification on wildlife communities is central to the development of conservation strategies. However, albeit male and female individuals of numerous species are known to exhibit differences in habitat use, sex‐specific responses to habitat modification remain little explored. Here, we used a landscape‐scale fragmentation experiment to assess, separately for males and females, the effects of fragmentation on the abundance of Carollia perspicillata and Rhinophylla pumilio, two widespread Neotropical frugivorous bats. We predicted that sex‐specific responses would arise from higher energetic requirements from pregnancy and lactation in females. Analyses were conducted independently for each season, and we further investigated the joint responses to local and landscape‐scale metrics of habitat quality, composition, and configuration. Although males and females responded similarly to a fragmentation gradient composed by continuous forest, fragment interiors, edges, and matrix habitats, we found marked differences between sexes in habitat use for at least one of the seasons. Whereas the sex ratio varied little in continuous forest and fragment interiors, females were found to be more abundant than males in edge and matrix habitats. This difference was more prominent in the dry season, the reproductive season of both species. For both species, abundance responses to local‐ and landscape‐scale predictors differed between sexes and again, differences were more pronounced in the dry season. The results suggest considerable sex‐mediated responses to forest disruption and degradation in tropical bats and complement our understanding of the impacts of fragmentation on tropical forest vertebrate communities.     

Response of wild mammals to seasonal shrinking-and-expansion of habitats due to flooding regime of the Pantanal, Brazil.

The Pantanal is a large savanna wetland (138,183 km2 in Brazil), important for its wildlife, fed by tributaries of the upper Paraguay River, center of South America (Brazil, touching Bolivia and Paraguay). Uplands are plateaus (250-1,200 m high, 215,000 km2 in Brazil) and flatland is the Pantanal (80-150 m high, 147,574 km2 in Brazil). Rivers are slow moving when they meet the flatland (slope 0.3-0.5 m/km east-west; 0.03-0.15 m/km north-south), periodically overflowing their banks, creating a complex seasonal habitat range. Recurrent shallow flooding occupies 80% of the Pantanal; during the dry season flooded areas dry up. Fluctuating water levels, nutrients and wildlife form a dynamic ecosystem. A flooding regime forms distinct sub-regions within the Pantanal. A mammal survey was carried out in the sub-region of the Rio Negro from April, 2003 through March, 2004 to study the diversity and abundance of terrestrial mammals during the dry and flooding seasons. A total of 36 species were observed in the field. The capybara Hydrochaeris hydrochaeris was the most frequent species, followed by the crab-eating-fox Cerdocyon thous and the marsh deer Blastocerus dichotomus. The highest abundance of species was observed during the dry season (August and September), when there is a considerable expansion of terrestrial habitats, mainly seasonally flooded grassland. Animal abundance (in terms of observed individual frequencies) varied during the dry and wet seasons and the seasonally flooded grassland was the most utilized habitat by mammals in the dry season.     

A new lineage of trypanosomes from Australian vertebrates and terrestrial bloodsucking leeches (Haemadipsidae)

Little is known about the trypanosomes of indigenous Australian vertebrates and their vectors. We surveyed a range of vertebrates and blood-feeding invertebrates for trypanosomes by parasitological and PCR-based methods using primers specific to the small subunit ribosomal RNA (SSU rRNA) gene of genus Trypanosoma. Trypanosome isolates were obtained in culture from two common wombats, one swamp wallaby and an Australian bird (Strepera sp.). By PCR, blood samples from three wombats, one brush-tailed wallaby, three platypuses and a frog were positive for trypanosome DNA. All the blood-sucking invertebrates screened were negative for trypanosomes both by microscopy and PCR, except for specimens of terrestrial leeches (Haemadipsidae). Of the latter, two Micobdella sp. specimens from Victoria and 18 Philaemon sp. specimens from Queensland were positive by PCR. Four Haemadipsa zeylanica specimens from Sri Lanka and three Leiobdella jawarerensis specimens from Papua New Guinea were also PCR positive for trypanosome DNA. We sequenced the SSU rRNA and glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) genes in order to determine the phylogenetic positions of the new vertebrate and terrestrial leech trypanosomes. In trees based on these genes, Australian vertebrate trypanosomes fell in several distinct clades, for the most part being more closely related to trypanosomes outside Australia than to each other. Two previously undescribed wallaby trypanosomes fell in a clade with Trypanosoma theileri, the cosmopolitan bovid trypanosome, and Trypanosoma cyclops from a Malaysian primate. The terrestrial leech trypanosomes were closely related to the wallaby trypanosomes, T. cyclops and a trypanosome from an Australian frog. We suggest that haemadipsid leeches may be significant and widespread vectors of trypanosomes in Australia and Asia.     

Habitat patch and matrix effects on small-mammal persistence in Amazonian forest fragments

Tropical forest mammal assemblages are widely affected by the twin effects of habitat loss and habitat fragmentation. We evaluated the effects of forest patch metrics, habitat structure, age of patch isolation, and landscape metrics on the species richness, abundance and composition of small mammals at 23 forest fragments (ranging in size from 43 to 7,035 ha) in a highly deforested 3,609-km² landscape of southwestern Brazilian Amazonia. Using pitfall traps and both terrestrial and arboreal traplines of Sherman, Tomahawk and snap traps, we captured a total of 844 individuals over 34,900 trap-nights representing 26 species and 20 genera of small-mammals, including 13 rodent and 13 marsupial species. We also consider the effects of distance from forest edges on species occupancy and abundance. Overall small mammal abundance, species richness and species composition were primarily affected by the quality of the open-habitat matrix of cattle pastures, rather than by patch metrics such as fragment size. Ultimately, small mammal community structure was determined by a combination of both landscape- and patch-scale variables. Knowledge of the anthropogenic factors that govern small mammal community structure is of critical importance for managing the persistence of forest vertebrates in increasingly fragmented neotropical forest landscapes.     

Effects of plant structure on butterfly diversity in Mt. Marsabit Forest – northern Kenya

Butterflies, like most forest dependent animals are good ecological indicators of the health of the forests they dwell. For example, butterfly species richness decreases after a forest disturbance and fragmentation but a few species may subsequently invade the forest fragment and boost the species richness. Studies were conducted to determine the effects of human activity and seasonal changes on butterfly species in the affected new habitats. Results showed that both seasonal and habitat changes significantly affect the butterfly abundance (P = 0.0001). Similarly, there was significant correlation between plant diversity and butterfly diversity in wet season (r = 0.854) and dry season (r = 0.855). The significance of these studies as a useful tool for sustainable forest use and conservation is discussed.